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2. An Out-of-Domain Synapse Detection Challenge for Microwasp Brain Connectomes

Author

Wu, Jingpeng, Li, Yicong, Gupta, Nishika, Shinomiya, Kazunori, Gunn, Pat, Polilov, Alexey, Pfister, Hanspeter, Chklovskii, Dmitri, and Wei, Donglai

Subjects
Computer Science - Computer Vision and Pattern Recognition, Quantitative Biology - Neurons and Cognition
Abstract

The size of image stacks in connectomics studies now reaches the terabyte and often petabyte scales with a great diversity of appearance across brain regions and samples. However, manual annotation of neural structures, e.g., synapses, is time-consuming, which leads to limited training data often smaller than 0.001\% of the test data in size. Domain adaptation and generalization approaches were proposed to address similar issues for natural images, which were less evaluated on connectomics data due to a lack of out-of-domain benchmarks.

Published
2023

4. A Connectome of the Male Drosophila Ventral Nerve Cord

Author

Takemura, Shin-ya, primary, Hayworth, Kenneth J, additional, Huang, Gary B, additional, Januszewski, Michal, additional, Lu, Zhiyuan, additional, Marin, Elizabeth C, additional, Preibisch, Stephan, additional, Xu, C Shan, additional, Bogovic, John, additional, Champion, Andrew S, additional, Cheong, Han SJ, additional, Costa, Marta, additional, Eichler, Katharina, additional, Katz, William, additional, Knecht, Christopher, additional, Li, Feng, additional, Morris, Billy J, additional, Ordish, Christopher, additional, Rivlin, Patricia K, additional, Schlegel, Philipp, additional, Shinomiya, Kazunori, additional, Stürner, Tomke, additional, Zhao, Ting, additional, Badalamente, Griffin, additional, Bailey, Dennis, additional, Brooks, Paul, additional, Canino, Brandon S, additional, Clements, Jody, additional, Cook, Michael, additional, Duclos, Octave, additional, Dunne, Christopher R, additional, Fairbanks, Kelli, additional, Fang, Siqi, additional, Finley-May, Samantha, additional, Francis, Audrey, additional, George, Reed, additional, Gkantia, Marina, additional, Harrington, Kyle, additional, Hopkins, Gary Patrick, additional, Hsu, Joseph, additional, Hubbard, Philip M, additional, Javier, Alexandre, additional, Kainmueller, Dagmar, additional, Korff, Wyatt, additional, Kovalyak, Julie, additional, Krzemiński, Dominik, additional, Lauchie, Shirley A, additional, Lohff, Alanna, additional, Maldonado, Charli, additional, Manley, Emily A, additional, Mooney, Caroline, additional, Neace, Erika, additional, Nichols, Matthew, additional, Ogundeyi, Omotara, additional, Okeoma, Nneoma, additional, Paterson, Tyler, additional, Phillips, Elliott, additional, Phillips, Emily M, additional, Ribeiro, Caitlin, additional, Ryan, Sean M, additional, Rymer, Jon Thomson, additional, Scott, Anne K, additional, Scott, Ashley L, additional, Shepherd, David, additional, Shinomiya, Aya, additional, Smith, Claire, additional, Smith, Natalie, additional, Suleiman, Alia, additional, Takemura, Satoko, additional, Talebi, Iris, additional, Tamimi, Imaan FM, additional, Trautman, Eric T, additional, Umayam, Lowell, additional, Walsh, John J, additional, Yang, Tansy, additional, Rubin, Gerald M, additional, Scheffer, Louis K, additional, Funke, Jan, additional, Saalfeld, Stephan, additional, Hess, Harald F, additional, Plaza, Stephen M, additional, Card, Gwyneth M, additional, Jefferis, Gregory SXE, additional, and Berg, Stuart, additional

Published
2024
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5. WASPSYN: A Challenge for Domain Adaptive Synapse Detection in Microwasp Brain Connectomes

Author

Li, Yicong, Li, Wanhua, Chen, Qi, Huang, Wei, Zou, Yuda, Xiao, Xin, Shinomiya, Kazunori, Gunn, Pat, Gupta, Nishika, Polilov, Alexey, Xu, Yongchao, Zhang, Yueyi, Xiong, Zhiwei, Pfister, Hanspeter, Wei, Donglai, and Wu, Jingpeng

Abstract

The size of image volumes in connectomics studies now reaches terabyte and often petabyte scales with a great diversity of appearance due to different sample preparation procedures. However, manual annotation of neuronal structures (e.g., synapses) in these huge image volumes is time-consuming, leading to limited labeled training data often smaller than 0.001% of the large-scale image volumes in application. Methods that can utilize in-domain labeled data and generalize to out-of-domain unlabeled data are in urgent need. Although many domain adaptation approaches are proposed to address such issues in the natural image domain, few of them have been evaluated on connectomics data due to a lack of domain adaptation benchmarks. Therefore, to enable developments of domain adaptive synapse detection methods for large-scale connectomics applications, we annotated 14 image volumes from a biologically diverse set of Megaphragma viggianii brain regions originating from three different whole-brain datasets and organized the WASPSYN challenge at ISBI 2023. The annotations include coordinates of pre-synapses and post-synapses in the 3D space, together with their one-to-many connectivity information. This paper describes the dataset, the tasks, the proposed baseline, the evaluation method, and the results of the challenge. Limitations of the challenge and the impact on neuroscience research are also discussed. The challenge is and will continue to be available at https://codalab.lisn.upsaclay.fr/competitions/9169. Successful algorithms that emerge from our challenge may potentially revolutionize real-world connectomics research and further the cause that aims to unravel the complexity of brain structure and function.

Published
2024
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6. Large-scale EM Analysis of the Drosophila Antennal Lobe with Automatically Computed Synapse Point Clouds

Author

Zhao, Ting, Takemura, Shin-ya, Huang, Gary B., Horne, Jane Anne, Katz, William T., Shinomiya, Kazunori, Scheffer, Louis K., Meinertzhagen, Ian A., Rivlin, Patricia K., and Plaza, Stephen M.

Subjects
Quantitative Biology - Quantitative Methods
Abstract

The promise of extracting connectomes and performing useful analysis on large electron microscopy (EM) datasets has been an elusive dream for many years. Tracing in even the smallest portions of neuropil requires copious human annotation, the rate-limiting step for generating a connectome. While a combination of improved imaging and automatic segmentation will lead to the analysis of increasingly large volumes, machines still fail to reach the quality of human tracers. Unfortunately, small errors in image segmentation can lead to catastrophic distortions of the connectome. In this paper, to analyze very large datasets, we explore different mechanisms that are less sensitive to errors in automation. Namely, we advocate and deploy extensive synapse detection on the entire antennal lobe (AL) neuropil in the brain of the fruit fly Drosophila, a region much larger than any densely annotated to date. The resulting synapse point cloud produced is invaluable for determining compartment boundaries in the AL and choosing specific regions for subsequent analysis. We introduce our methodology in this paper for region selection and show both manual and automatic synapse annotation results. Finally, we note the correspondence between image datasets obtained using the synaptic marker, antibody nc82, and our datasets enabling registration between light and EM image modalities.

Published
2015

7. A Systematic Nomenclature for the Insect Brain

Author

Ito, Kei, Shinomiya, Kazunori, Ito, Masayoshi, Armstrong, J Douglas, Boyan, George, Hartenstein, Volker, Harzsch, Steffen, Heisenberg, Martin, Homberg, Uwe, Jenett, Arnim, Keshishian, Haig, Restifo, Linda L, Rössler, Wolfgang, Simpson, Julie H, Strausfeld, Nicholas J, Strauss, Roland, Vosshall, Leslie B, and Group, Insect Brain Name Working

Subjects
Neurosciences, Underpinning research, 1.1 Normal biological development and functioning, Neurological, Animals, Brain, Drosophila melanogaster, Female, Neural Pathways, Neuropil, Terminology as Topic, Insect Brain Name Working Group, Psychology, Cognitive Sciences, Neurology & Neurosurgery
Abstract

Despite the importance of the insect nervous system for functional and developmental neuroscience, descriptions of insect brains have suffered from a lack of uniform nomenclature. Ambiguous definitions of brain regions and fiber bundles have contributed to the variation of names used to describe the same structure. The lack of clearly determined neuropil boundaries has made it difficult to document precise locations of neuronal projections for connectomics study. To address such issues, a consortium of neurobiologists studying arthropod brains, the Insect Brain Name Working Group, has established the present hierarchical nomenclature system, using the brain of Drosophila melanogaster as the reference framework, while taking the brains of other taxa into careful consideration for maximum consistency and expandability. The following summarizes the consortium's nomenclature system and highlights examples of existing ambiguities and remedies for them. This nomenclature is intended to serve as a standard of reference for the study of the brain of Drosophila and other insects.

Published
2014

9. Connectome-constrained deep mechanistic networks predict neural responses across the fly visual system at single-neuron resolution

Author

Lappalainen, Janne K., Tschopp, Fabian D., Prakhya, Sridhama, McGill, Mason, Nern, Aljoscha, Shinomiya, Kazunori, Takemura, Shin-ya, Gruntman, Eyal, Macke, Jakob H., Turaga, Srinivas C., Lappalainen, Janne K., Tschopp, Fabian D., Prakhya, Sridhama, McGill, Mason, Nern, Aljoscha, Shinomiya, Kazunori, Takemura, Shin-ya, Gruntman, Eyal, Macke, Jakob H., and Turaga, Srinivas C.

Abstract

We can now measure the connectivity of every neuron in a neural circuit, but we are still blind to other biological details, including the dynamical characteristics of each neuron. The degree to which connectivity measurements alone can inform understanding of neural computation is an open question. Here we show that with only measurements of the connectivity of a biological neural network, we can predict the neural activity underlying neural computation. We constructed a model neural network with the experimentally determined connectivity for 64 cell types in the motion pathways of the fruit fly optic lobe but with unknown parameters for the single neuron and single synapse properties. We then optimized the values of these unknown parameters using techniques from deep learning, to allow the model network to detect visual motion. Our mechanistic model makes detailed experimentally testable predictions for each neuron in the connectome. We found that model predictions agreed with experimental measurements of neural activity across 24 studies. Our work demonstrates a strategy for generating detailed hypotheses about the mechanisms of neural circuit function from connectivity measurements. We show that this strategy is more likely to be successful when neurons are sparsely connected---a universally observed feature of biological neural networks across species and brain regions.

Published
2023

14. A connectome and analysis of the adult Drosophila central brain

Author

Scheffer, Louis K., Xu, C. Shan, Januszewski, Michal, Lu, Zhiyuan, Takemura, Shin-ya, Hayworth, Kenneth J., Huang, Gary B., Shinomiya, Kazunori, Maitlin-Shepard, Jeremy, Berg, Stuart, Clements, Jody, Hubbard, Philip M., Katz, William T., Umayam, Lowell, Zhao, Ting, Ackerman, David, Blakely, Tim, Bogovic, John, Dolafi, Tom, Kainmueller, Dagmar, Kawase, Takashi, Khairy, Khaled A., Leavitt, Laramie, Li, Peter H., Lindsey, Larry, Neubarth, Nicole, Olbris, Donald J., Otsuna, Hideo, Trautman, Eric T., Ito, Masayoshi, Bates, Alexander S., Goldammer, Jens, Wolff, Tanya, Svirskas, Robert, Schlegel, Philipp, Neace, Erika, Knecht, Christopher J., Alvarado, Chelsea X., Bailey, Dennis A., Ballinger, Samantha, Borycz, Jolanta A., Canino, Brandon S., Cheatham, Natasha, Cook, Michael, Dreher, Marisa, Duclos, Octave, Eubanks, Bryon, Fairbanks, Kelli, Finley, Samantha, Forknall, Nora, Francis, Audrey, Hopkins, Gary Patrick, Joyce, Emily M., Kim, SungJin, Kirk, Nicole A., Kovalyak, Julie, Lauchie, Shirley A., Lohff, Alanna, Maldonado, Charli, Manley, Emily A., McLin, Sari, Mooney, Caroline, Ndama, Miatta, Ogundeyi, Omotara, Okeoma, Nneoma, Ordish, Christopher, Padilla, Nicholas, Patrick, Christopher M., Paterson, Tyler, Phillips, Elliott E., Phillips, Emily M., Rampally, Neha, Ribeiro, Caitlin, Robertson, Madelaine K., Rymer, Jon Thomson, Ryan, Sean M., Sammons, Megan, Scott, Anne K., Scott, Ashley L., Shinomiya, Aya, Smith, Claire, Smith, Kelsey, Smith, Natalie L., Sobeski, Margaret A., Suleiman, Alia, Swift, Jackie, Takemura, Satoko, Talebi, Iris, Tarnogorska, Dorota, Tenshaw, Emily, Tokhi, Temour, Walsh, John J., Yang, Tansy, Horne, Jane Anne, Li, Feng, Parekh, Ruchi, Rivlin, Patricia K., Jayaraman, Vivek, Costa, Marta, Jefferis, Gregory S. X. E., Ito, Kei, Saalfeld, Stephan, George, Reed, Meinertzhagen, Ian A., Rubin, Gerald M., Hess, Harald F., Jain, Viren, Plaza, Stephen M., Scheffer, Louis K., Xu, C. Shan, Januszewski, Michal, Lu, Zhiyuan, Takemura, Shin-ya, Hayworth, Kenneth J., Huang, Gary B., Shinomiya, Kazunori, Maitlin-Shepard, Jeremy, Berg, Stuart, Clements, Jody, Hubbard, Philip M., Katz, William T., Umayam, Lowell, Zhao, Ting, Ackerman, David, Blakely, Tim, Bogovic, John, Dolafi, Tom, Kainmueller, Dagmar, Kawase, Takashi, Khairy, Khaled A., Leavitt, Laramie, Li, Peter H., Lindsey, Larry, Neubarth, Nicole, Olbris, Donald J., Otsuna, Hideo, Trautman, Eric T., Ito, Masayoshi, Bates, Alexander S., Goldammer, Jens, Wolff, Tanya, Svirskas, Robert, Schlegel, Philipp, Neace, Erika, Knecht, Christopher J., Alvarado, Chelsea X., Bailey, Dennis A., Ballinger, Samantha, Borycz, Jolanta A., Canino, Brandon S., Cheatham, Natasha, Cook, Michael, Dreher, Marisa, Duclos, Octave, Eubanks, Bryon, Fairbanks, Kelli, Finley, Samantha, Forknall, Nora, Francis, Audrey, Hopkins, Gary Patrick, Joyce, Emily M., Kim, SungJin, Kirk, Nicole A., Kovalyak, Julie, Lauchie, Shirley A., Lohff, Alanna, Maldonado, Charli, Manley, Emily A., McLin, Sari, Mooney, Caroline, Ndama, Miatta, Ogundeyi, Omotara, Okeoma, Nneoma, Ordish, Christopher, Padilla, Nicholas, Patrick, Christopher M., Paterson, Tyler, Phillips, Elliott E., Phillips, Emily M., Rampally, Neha, Ribeiro, Caitlin, Robertson, Madelaine K., Rymer, Jon Thomson, Ryan, Sean M., Sammons, Megan, Scott, Anne K., Scott, Ashley L., Shinomiya, Aya, Smith, Claire, Smith, Kelsey, Smith, Natalie L., Sobeski, Margaret A., Suleiman, Alia, Swift, Jackie, Takemura, Satoko, Talebi, Iris, Tarnogorska, Dorota, Tenshaw, Emily, Tokhi, Temour, Walsh, John J., Yang, Tansy, Horne, Jane Anne, Li, Feng, Parekh, Ruchi, Rivlin, Patricia K., Jayaraman, Vivek, Costa, Marta, Jefferis, Gregory S. X. E., Ito, Kei, Saalfeld, Stephan, George, Reed, Meinertzhagen, Ian A., Rubin, Gerald M., Hess, Harald F., Jain, Viren, and Plaza, Stephen M.

Abstract

The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine computational compartments, and provide an exhaustive atlas of cell examples and types, many of them novel. We provide detailed circuits consisting of neurons and their chemical synapses for most of the central brain. We make the data public and simplify access, reducing the effort needed eLife digest Animal brains of all sizes, from the smallest to the largest, work in broadly similar ways. Studying the brain of any one animal in depth can thus reveal the general principles behind the workings of all brains. The fruit fly Drosophila is a popular choice for such research. With about 100,000 neurons - compared to some 86 billion in humans - the fly brain is small enough to study at the level of individual cells. But it nevertheless supports a range of complex behaviors, including navigation, courtship and learning. Thanks to decades of research, scientists now have a good understanding of which parts of the fruit fly brain support particular behaviors. But exactly how they do this is often unclear. This is because previous studies showing the connections between cells only covered small areas of the brain. This is like trying to understand a novel when all you can see is a few isolated paragraphs. To solve this problem, Scheffer, Xu, Januszewski, Lu, Takemura, Hayworth, Huang, Shinomiya et al. prepared the first complete map of the entire central region of the fruit fly brain. The central brain consists of approximately 25,000 neurons and around 20 million connections. To prepare the map - or connectome - the brain was cut into very thin 8nm slices and photographed with an electron microscope. A three-dimensional

Published
2020

16. A connectome and analysis of the adult Drosophila central brain

Author

Scheffer, Louis K, primary, Xu, C Shan, additional, Januszewski, Michal, additional, Lu, Zhiyuan, additional, Takemura, Shin-ya, additional, Hayworth, Kenneth J, additional, Huang, Gary B, additional, Shinomiya, Kazunori, additional, Maitlin-Shepard, Jeremy, additional, Berg, Stuart, additional, Clements, Jody, additional, Hubbard, Philip M, additional, Katz, William T, additional, Umayam, Lowell, additional, Zhao, Ting, additional, Ackerman, David, additional, Blakely, Tim, additional, Bogovic, John, additional, Dolafi, Tom, additional, Kainmueller, Dagmar, additional, Kawase, Takashi, additional, Khairy, Khaled A, additional, Leavitt, Laramie, additional, Li, Peter H, additional, Lindsey, Larry, additional, Neubarth, Nicole, additional, Olbris, Donald J, additional, Otsuna, Hideo, additional, Trautman, Eric T, additional, Ito, Masayoshi, additional, Bates, Alexander S, additional, Goldammer, Jens, additional, Wolff, Tanya, additional, Svirskas, Robert, additional, Schlegel, Philipp, additional, Neace, Erika, additional, Knecht, Christopher J, additional, Alvarado, Chelsea X, additional, Bailey, Dennis A, additional, Ballinger, Samantha, additional, Borycz, Jolanta A, additional, Canino, Brandon S, additional, Cheatham, Natasha, additional, Cook, Michael, additional, Dreher, Marisa, additional, Duclos, Octave, additional, Eubanks, Bryon, additional, Fairbanks, Kelli, additional, Finley, Samantha, additional, Forknall, Nora, additional, Francis, Audrey, additional, Hopkins, Gary Patrick, additional, Joyce, Emily M, additional, Kim, SungJin, additional, Kirk, Nicole A, additional, Kovalyak, Julie, additional, Lauchie, Shirley A, additional, Lohff, Alanna, additional, Maldonado, Charli, additional, Manley, Emily A, additional, McLin, Sari, additional, Mooney, Caroline, additional, Ndama, Miatta, additional, Ogundeyi, Omotara, additional, Okeoma, Nneoma, additional, Ordish, Christopher, additional, Padilla, Nicholas, additional, Patrick, Christopher M, additional, Paterson, Tyler, additional, Phillips, Elliott E, additional, Phillips, Emily M, additional, Rampally, Neha, additional, Ribeiro, Caitlin, additional, Robertson, Madelaine K, additional, Rymer, Jon Thomson, additional, Ryan, Sean M, additional, Sammons, Megan, additional, Scott, Anne K, additional, Scott, Ashley L, additional, Shinomiya, Aya, additional, Smith, Claire, additional, Smith, Kelsey, additional, Smith, Natalie L, additional, Sobeski, Margaret A, additional, Suleiman, Alia, additional, Swift, Jackie, additional, Takemura, Satoko, additional, Talebi, Iris, additional, Tarnogorska, Dorota, additional, Tenshaw, Emily, additional, Tokhi, Temour, additional, Walsh, John J, additional, Yang, Tansy, additional, Horne, Jane Anne, additional, Li, Feng, additional, Parekh, Ruchi, additional, Rivlin, Patricia K, additional, Jayaraman, Vivek, additional, Costa, Marta, additional, Jefferis, Gregory SXE, additional, Ito, Kei, additional, Saalfeld, Stephan, additional, George, Reed, additional, Meinertzhagen, Ian A, additional, Rubin, Gerald M, additional, Hess, Harald F, additional, Jain, Viren, additional, and Plaza, Stephen M, additional

Published
2020
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17. Author response: A connectome and analysis of the adult Drosophila central brain

Author

Scheffer, Louis K, primary, Xu, C Shan, additional, Januszewski, Michal, additional, Lu, Zhiyuan, additional, Takemura, Shin-ya, additional, Hayworth, Kenneth J, additional, Huang, Gary B, additional, Shinomiya, Kazunori, additional, Maitlin-Shepard, Jeremy, additional, Berg, Stuart, additional, Clements, Jody, additional, Hubbard, Philip M, additional, Katz, William T, additional, Umayam, Lowell, additional, Zhao, Ting, additional, Ackerman, David, additional, Blakely, Tim, additional, Bogovic, John, additional, Dolafi, Tom, additional, Kainmueller, Dagmar, additional, Kawase, Takashi, additional, Khairy, Khaled A, additional, Leavitt, Laramie, additional, Li, Peter H, additional, Lindsey, Larry, additional, Neubarth, Nicole, additional, Olbris, Donald J, additional, Otsuna, Hideo, additional, Trautman, Eric T, additional, Ito, Masayoshi, additional, Bates, Alexander S, additional, Goldammer, Jens, additional, Wolff, Tanya, additional, Svirskas, Robert, additional, Schlegel, Philipp, additional, Neace, Erika, additional, Knecht, Christopher J, additional, Alvarado, Chelsea X, additional, Bailey, Dennis A, additional, Ballinger, Samantha, additional, Borycz, Jolanta A, additional, Canino, Brandon S, additional, Cheatham, Natasha, additional, Cook, Michael, additional, Dreher, Marisa, additional, Duclos, Octave, additional, Eubanks, Bryon, additional, Fairbanks, Kelli, additional, Finley, Samantha, additional, Forknall, Nora, additional, Francis, Audrey, additional, Hopkins, Gary Patrick, additional, Joyce, Emily M, additional, Kim, SungJin, additional, Kirk, Nicole A, additional, Kovalyak, Julie, additional, Lauchie, Shirley A, additional, Lohff, Alanna, additional, Maldonado, Charli, additional, Manley, Emily A, additional, McLin, Sari, additional, Mooney, Caroline, additional, Ndama, Miatta, additional, Ogundeyi, Omotara, additional, Okeoma, Nneoma, additional, Ordish, Christopher, additional, Padilla, Nicholas, additional, Patrick, Christopher M, additional, Paterson, Tyler, additional, Phillips, Elliott E, additional, Phillips, Emily M, additional, Rampally, Neha, additional, Ribeiro, Caitlin, additional, Robertson, Madelaine K, additional, Rymer, Jon Thomson, additional, Ryan, Sean M, additional, Sammons, Megan, additional, Scott, Anne K, additional, Scott, Ashley L, additional, Shinomiya, Aya, additional, Smith, Claire, additional, Smith, Kelsey, additional, Smith, Natalie L, additional, Sobeski, Margaret A, additional, Suleiman, Alia, additional, Swift, Jackie, additional, Takemura, Satoko, additional, Talebi, Iris, additional, Tarnogorska, Dorota, additional, Tenshaw, Emily, additional, Tokhi, Temour, additional, Walsh, John J, additional, Yang, Tansy, additional, Horne, Jane Anne, additional, Li, Feng, additional, Parekh, Ruchi, additional, Rivlin, Patricia K, additional, Jayaraman, Vivek, additional, Costa, Marta, additional, Jefferis, Gregory SXE, additional, Ito, Kei, additional, Saalfeld, Stephan, additional, George, Reed, additional, Meinertzhagen, Ian A, additional, Rubin, Gerald M, additional, Hess, Harald F, additional, Jain, Viren, additional, and Plaza, Stephen M, additional

Published
2020
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18. A Connectome and Analysis of the Adult Drosophila Central Brain

Author

Scheffer, Louis K., primary, Xu, C. Shan, additional, Januszewski, Michal, additional, Lu, Zhiyuan, additional, Takemura, Shin-ya, additional, Hayworth, Kenneth J., additional, Huang, Gary B., additional, Shinomiya, Kazunori, additional, Maitin-Shepard, Jeremy, additional, Berg, Stuart, additional, Clements, Jody, additional, Hubbard, Philip, additional, Katz, William, additional, Umayam, Lowell, additional, Zhao, Ting, additional, Ackerman, David, additional, Blakely, Tim, additional, Bogovic, John, additional, Dolafi, Tom, additional, Kainmueller, Dagmar, additional, Kawase, Takashi, additional, Khairy, Khaled A., additional, Leavitt, Laramie, additional, Li, Peter H., additional, Lindsey, Larry, additional, Neubarth, Nicole, additional, Olbris, Donald J., additional, Otsuna, Hideo, additional, Trautman, Eric T., additional, Ito, Masayoshi, additional, Goldammer, Jens, additional, Wolff, Tanya, additional, Svirskas, Robert, additional, Schlegel, Philipp, additional, Neace, Erika R., additional, Knecht, Christopher J., additional, Alvarado, Chelsea X., additional, Bailey, Dennis A., additional, Ballinger, Samantha, additional, Borycz, Jolanta A, additional, Canino, Brandon S., additional, Cheatham, Natasha, additional, Cook, Michael, additional, Dreher, Marisa, additional, Duclos, Octave, additional, Eubanks, Bryon, additional, Fairbanks, Kelli, additional, Finley, Samantha, additional, Forknall, Nora, additional, Francis, Audrey, additional, Hopkins, Gary Patrick, additional, Joyce, Emily M., additional, Kim, SungJin, additional, Kirk, Nicole A., additional, Kovalyak, Julie, additional, Lauchie, Shirley A., additional, Lohff, Alanna, additional, Maldonado, Charli, additional, Manley, Emily A., additional, McLin, Sari, additional, Mooney, Caroline, additional, Ndama, Miatta, additional, Ogundeyi, Omotara, additional, Okeoma, Nneoma, additional, Ordish, Christopher, additional, Padilla, Nicholas, additional, Patrick, Christopher, additional, Paterson, Tyler, additional, Phillips, Elliott E., additional, Phillips, Emily M., additional, Rampally, Neha, additional, Ribeiro, Caitlin, additional, Robertson, Madelaine K, additional, Rymer, Jon Thomson, additional, Ryan, Sean M., additional, Sammons, Megan, additional, Scott, Anne K., additional, Scott, Ashley L., additional, Shinomiya, Aya, additional, Smith, Claire, additional, Smith, Kelsey, additional, Smith, Natalie L., additional, Sobeski, Margaret A., additional, Suleiman, Alia, additional, Swift, Jackie, additional, Takemura, Satoko, additional, Talebi, Iris, additional, Tarnogorska, Dorota, additional, Tenshaw, Emily, additional, Tokhi, Temour, additional, Walsh, John J., additional, Yang, Tansy, additional, Horne, Jane Anne, additional, Li, Feng, additional, Parekh, Ruchi, additional, Rivlin, Patricia K., additional, Jayaraman, Vivek, additional, Ito, Kei, additional, Saalfeld, Stephan, additional, George, Reed, additional, Meinertzhagen, Ian A., additional, Rubin, Gerald M., additional, Hess, Harald F., additional, Jain, Viren, additional, and Plaza, Stephen M., additional

Published
2020
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19. A Connectome of the Adult Drosophila Central Brain

Author

Xu, C. Shan, primary, Januszewski, Michal, additional, Lu, Zhiyuan, additional, Takemura, Shin-ya, additional, Hayworth, Kenneth J., additional, Huang, Gary, additional, Shinomiya, Kazunori, additional, Maitin-Shepard, Jeremy, additional, Ackerman, David, additional, Berg, Stuart, additional, Blakely, Tim, additional, Bogovic, John, additional, Clements, Jody, additional, Dolafi, Tom, additional, Hubbard, Philip, additional, Kainmueller, Dagmar, additional, Katz, William, additional, Kawase, Takashi, additional, Khairy, Khaled A., additional, Leavitt, Laramie, additional, Li, Peter H., additional, Lindsey, Larry, additional, Neubarth, Nicole, additional, Olbris, Donald J., additional, Otsuna, Hideo, additional, Troutman, Eric T., additional, Umayam, Lowell, additional, Zhao, Ting, additional, Ito, Masayoshi, additional, Goldammer, Jens, additional, Wolff, Tanya, additional, Svirskas, Robert, additional, Schlegel, Philipp, additional, Neace, Erika R., additional, Knecht, Christopher J., additional, Alvarado, Chelsea X., additional, Bailey, Dennis A., additional, Ballinger, Samantha, additional, Borycz, Jolanta A, additional, Canino, Brandon S., additional, Cheatham, Natasha, additional, Cook, Michael, additional, Dreher, Marisa, additional, Duclos, Octave, additional, Eubanks, Bryon, additional, Fairbanks, Kelli, additional, Finley, Samantha, additional, Forknall, Nora, additional, Francis, Audrey, additional, Hopkins, Gary Patrick, additional, Joyce, Emily M., additional, Kim, SungJin, additional, Kirk, Nicole A., additional, Kovalyak, Julie, additional, Lauchie, Shirley A., additional, Lohff, Alanna, additional, Maldonado, Charli, additional, Manley, Emily A., additional, McLin, Sari, additional, Mooney, Caroline, additional, Ndama, Miatta, additional, Ogundeyi, Omotara, additional, Okeoma, Nneoma, additional, Ordish, Christopher, additional, Padilla, Nicholas, additional, Patrick, Christopher, additional, Paterson, Tyler, additional, Phillips, Elliott E., additional, Phillips, Emily M., additional, Rampally, Neha, additional, Ribeiro, Caitlin, additional, Robertson, Madelaine K, additional, Rymer, Jon Thomson, additional, Ryan, Sean M., additional, Sammons, Megan, additional, Scott, Anne K., additional, Scott, Ashley L., additional, Shinomiya, Aya, additional, Smith, Claire, additional, Smith, Kelsey, additional, Smith, Natalie L., additional, Sobeski, Margaret A., additional, Suleiman, Alia, additional, Swift, Jackie, additional, Takemura, Satoko, additional, Talebi, Iris, additional, Tarnogorska, Dorota, additional, Tenshaw, Emily, additional, Tokhi, Temour, additional, Walsh, John J., additional, Yang, Tansy, additional, Horne, Jane Anne, additional, Li, Feng, additional, Parekh, Ruchi, additional, Rivlin, Patricia K., additional, Jayaraman, Vivek, additional, Ito, Kei, additional, Saalfeld, Stephan, additional, George, Reed, additional, Meinertzhagen, Ian, additional, Rubin, Gerald M., additional, Hess, Harald F., additional, Scheffer, Louis K., additional, Jain, Viren, additional, and Plaza, Stephen M., additional

Published
2020
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21. Comparisons between the ON- and OFF-edge motion pathways in the Drosophila brain

Author

Shinomiya, Kazunori, primary, Huang, Gary, additional, Lu, Zhiyuan, additional, Parag, Toufiq, additional, Xu, C Shan, additional, Aniceto, Roxanne, additional, Ansari, Namra, additional, Cheatham, Natasha, additional, Lauchie, Shirley, additional, Neace, Erika, additional, Ogundeyi, Omotara, additional, Ordish, Christopher, additional, Peel, David, additional, Shinomiya, Aya, additional, Smith, Claire, additional, Takemura, Satoko, additional, Talebi, Iris, additional, Rivlin, Patricia K, additional, Nern, Aljoscha, additional, Scheffer, Louis K, additional, Plaza, Stephen M, additional, and Meinertzhagen, Ian A, additional

Published
2019
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22. Author response: Comparisons between the ON- and OFF-edge motion pathways in the Drosophila brain

Author

Shinomiya, Kazunori, primary, Huang, Gary, additional, Lu, Zhiyuan, additional, Parag, Toufiq, additional, Xu, C Shan, additional, Aniceto, Roxanne, additional, Ansari, Namra, additional, Cheatham, Natasha, additional, Lauchie, Shirley, additional, Neace, Erika, additional, Ogundeyi, Omotara, additional, Ordish, Christopher, additional, Peel, David, additional, Shinomiya, Aya, additional, Smith, Claire, additional, Takemura, Satoko, additional, Talebi, Iris, additional, Rivlin, Patricia K, additional, Nern, Aljoscha, additional, Scheffer, Louis K, additional, Plaza, Stephen M, additional, and Meinertzhagen, Ian A, additional

Published
2018
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23. Comparisons between the ON- and OFFedge motion pathways in the Drosophila brain.

Author

Shinomiya, Kazunori, Huang, Gary, Lu, Zhiyuan, Parag, Toufiq, Xu, C Shan, Aniceto, Roxanne, Ansari, Namra, Cheatham, Natasha, Lauchie, Shirley, Neace, Erika, Ogundeyi, Omotara, Ordish, Christopher, Peel, David, Shinomiya, Aya, Smith, Claire, Takemura, Satoko, Talebi, Iris, Rivlin, Patricia K., Nern, Aljoscha, and Scheffer, Louis K.

Abstract

Understanding the circuit mechanisms behind motion detection is a long-standing question in visual neuroscience. In Drosophila melanogaster, recently discovered synapse-level connectomes in the optic lobe, particularly in ON-pathway (T4) receptive-field circuits, in concert with physiological studies, suggest a motion model that is increasingly intricate when compared with the ubiquitous Hassenstein-Reichardt model. By contrast, our knowledge of OFF-pathway (T5) has been incomplete. Here, we present a conclusive and comprehensive connectome that, for the first time, integrates detailed connectivity information for inputs to both the T4 and T5 pathways in a single EM dataset covering the entire optic lobe. With novel reconstruction methods using automated synapse prediction suited to such a large connectome, we successfully corroborate previous findings in the T4 pathway and comprehensively identify inputs and receptive fields for T5. Although the two pathways are probably evolutionarily linked and exhibit many similarities, we uncover interesting differences and interactions that may underlie their distinct functional properties. [ABSTRACT FROM AUTHOR]

Published
2019
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32. A connectome and analysis of the adult Drosophila central brain

Author

Temour Tokhi, Tom Dolafi, Nneoma Okeoma, Tanya Wolff, Philip M Hubbard, Kazunori Shinomiya, Madelaine K Robertson, Gerald M. Rubin, Gregory S.X.E. Jefferis, Christopher J Knecht, Laramie Leavitt, Alia Suleiman, Satoko Takemura, Christopher Ordish, Jody Clements, Ian A. Meinertzhagen, Alexander Shakeel Bates, Takashi Kawase, Samantha Finley, Nicholas Padilla, Jackie Swift, C. Shan Xu, Stuart Berg, Tyler Paterson, Ashley L Scott, Erika Neace, Shirley Lauchie, Sean M Ryan, Emily M Joyce, Shin-ya Takemura, Tim Blakely, Michael A Cook, Christopher Patrick, Bryon Eubanks, Audrey Francis, Robert Svirskas, William T. Katz, Eric T. Trautman, Caroline Mooney, Ting Zhao, Nicole A Kirk, Megan Sammons, Brandon S Canino, Reed A. George, Louis K. Scheffer, Jolanta A. Borycz, Jon Thomson Rymer, Natasha Cheatham, Dagmar Kainmueller, Gary B. Huang, Khaled Khairy, Nicole Neubarth, Elliott E Phillips, John A. Bogovic, Neha Rampally, Larry Lindsey, Viren Jain, David G. Ackerman, Jane Anne Horne, Kelli Fairbanks, Lowell Umayam, Jens Goldammer, Emily M Phillips, Donald J. Olbris, Feng Li, Emily A Manley, Philipp Schlegel, Hideo Otsuna, Marta Costa, Stephen M. Plaza, Omotara Ogundeyi, Samantha Ballinger, Charli Maldonado, Kelsey Smith, Gary Patrick Hopkins, Vivek Jayaraman, Emily Tenshaw, Julie Kovalyak, Peter H. Li, Tansy Yang, Masayoshi Ito, Miatta Ndama, Claire Smith, Michał Januszewski, Alanna Lohff, SungJin Kim, Anne K Scott, Kei Ito, Iris Talebi, Jeremy Maitlin-Shepard, Nora Forknall, Marisa Dreher, Harald F. Hess, Sari McLin, Patricia K. Rivlin, Dennis A Bailey, Kenneth J. Hayworth, Octave Duclos, Caitlin Ribeiro, John J. Walsh, Zhiyuan Lu, Dorota Tarnogorska, Ruchi Parekh, Aya Shinomiya, Stephan Saalfeld, Margaret A Sobeski, Natalie L Smith, Chelsea X Alvarado, Scheffer, Louis K [0000-0002-3289-6564], Xu, C Shan [0000-0002-8564-7836], Januszewski, Michal [0000-0002-3480-2744], Lu, Zhiyuan [0000-0002-4128-9774], Takemura, Shin-ya [0000-0003-2400-6426], Huang, Gary B [0000-0002-9606-3510], Shinomiya, Kazunori [0000-0003-0262-6421], Maitlin-Shepard, Jeremy [0000-0001-8453-7961], Hubbard, Philip M [0000-0002-6746-5035], Katz, William T [0000-0002-9417-6212], Ackerman, David [0000-0003-0172-6594], Blakely, Tim [0000-0003-0995-5471], Bogovic, John [0000-0002-4829-9457], Kainmueller, Dagmar [0000-0002-9830-2415], Khairy, Khaled A [0000-0002-9274-5928], Li, Peter H [0000-0001-6193-4454], Trautman, Eric T [0000-0001-8588-0569], Bates, Alexander S [0000-0002-1195-0445], Goldammer, Jens [0000-0002-5623-8339], Wolff, Tanya [0000-0002-8681-1749], Svirskas, Robert [0000-0001-8374-6008], Schlegel, Philipp [0000-0002-5633-1314], Knecht, Christopher J [0000-0002-5663-5967], Alvarado, Chelsea X [0000-0002-5973-7512], Bailey, Dennis A [0000-0002-4675-8373], Borycz, Jolanta A [0000-0002-4402-9230], Canino, Brandon S [0000-0002-8454-865X], Cook, Michael [0000-0002-7892-6845], Dreher, Marisa [0000-0002-0041-9229], Eubanks, Bryon [0000-0002-9288-2009], Fairbanks, Kelli [0000-0002-6601-4830], Finley, Samantha [0000-0002-8086-206X], Forknall, Nora [0000-0003-2139-7599], Francis, Audrey [0000-0003-1974-7174], Joyce, Emily M [0000-0001-5794-6321], Kovalyak, Julie [0000-0001-7864-7734], Lauchie, Shirley A [0000-0001-8223-9522], Lohff, Alanna [0000-0002-1242-1836], McLin, Sari [0000-0002-9120-1136], Patrick, Christopher M [0000-0001-8830-1892], Phillips, Elliott E [0000-0002-4918-2058], Phillips, Emily M [0000-0001-7615-301X], Robertson, Madelaine K [0000-0002-1764-0245], Rymer, Jon Thomson [0000-0002-4271-6774], Ryan, Sean M [0000-0002-8879-6108], Sammons, Megan [0000-0003-4516-5928], Shinomiya, Aya [0000-0002-6358-9567], Smith, Natalie L [0000-0002-8271-9873], Swift, Jackie [0000-0003-1321-8183], Takemura, Satoko [0000-0002-2863-0050], Talebi, Iris [0000-0002-0173-8053], Tarnogorska, Dorota [0000-0002-7063-6165], Walsh, John J [0000-0002-7176-4708], Yang, Tansy [0000-0003-1131-0410], Horne, Jane Anne [0000-0001-9673-2692], Parekh, Ruchi [0000-0002-8060-2807], Jayaraman, Vivek [0000-0003-3680-7378], Costa, Marta [0000-0001-5948-3092], Jefferis, Gregory SXE [0000-0002-0587-9355], Ito, Kei [0000-0002-7274-5533], Saalfeld, Stephan [0000-0002-4106-1761], Rubin, Gerald M [0000-0001-8762-8703], Hess, Harald F [0000-0003-3000-1533], Plaza, Stephen M [0000-0001-7425-8555], Apollo - University of Cambridge Repository, Takemura, Shin-Ya [0000-0003-2400-6426], and Jefferis, Gregory Sxe [0000-0002-0587-9355]

Subjects
Male, Computer science, computational biology, 0302 clinical medicine, Drosophila Proteins, Research article, Biology (General), Neurons, Cognitive science, 0303 health sciences, biology, D. melanogaster, General Neuroscience, connectome, Brain, systems biology, graph properties, General Medicine, Human brain, Drosophila melanogaster, medicine.anatomical_structure, Connectome, Medicine, Drosophila, Female, synapse detecton, Insight, Function and Dysfunction of the Nervous System, cell types, Research Article, Computational and Systems Biology, brain regions, Connectomes, QH301-705.5, Ubiquitin-Protein Ligases, Science, connectome reconstuction methods, Small mammal, Central region, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, medicine, Animals, 030304 developmental biology, General Immunology and Microbiology, biology.organism_classification, synapse detection, Synapses, 030217 neurology & neurosurgery, Neuroscience
Abstract

The neural circuits responsible for animal behavior remain largely unknown. We summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, segment, find synapses in, and proofread such large data sets. We define cell types, refine computational compartments, and provide an exhaustive atlas of cell examples and types, many of them novel. We provide detailed circuits consisting of neurons and their chemical synapses for most of the central brain. We make the data public and simplify access, reducing the effort needed to answer circuit questions, and provide procedures linking the neurons defined by our analysis with genetic reagents. Biologically, we examine distributions of connection strengths, neural motifs on different scales, electrical consequences of compartmentalization, and evidence that maximizing packing density is an important criterion in the evolution of the fly’s brain., eLife digest Animal brains of all sizes, from the smallest to the largest, work in broadly similar ways. Studying the brain of any one animal in depth can thus reveal the general principles behind the workings of all brains. The fruit fly Drosophila is a popular choice for such research. With about 100,000 neurons – compared to some 86 billion in humans – the fly brain is small enough to study at the level of individual cells. But it nevertheless supports a range of complex behaviors, including navigation, courtship and learning. Thanks to decades of research, scientists now have a good understanding of which parts of the fruit fly brain support particular behaviors. But exactly how they do this is often unclear. This is because previous studies showing the connections between cells only covered small areas of the brain. This is like trying to understand a novel when all you can see is a few isolated paragraphs. To solve this problem, Scheffer, Xu, Januszewski, Lu, Takemura, Hayworth, Huang, Shinomiya et al. prepared the first complete map of the entire central region of the fruit fly brain. The central brain consists of approximately 25,000 neurons and around 20 million connections. To prepare the map – or connectome – the brain was cut into very thin 8nm slices and photographed with an electron microscope. A three-dimensional map of the neurons and connections in the brain was then reconstructed from these images using machine learning algorithms. Finally, Scheffer et al. used the new connectome to obtain further insights into the circuits that support specific fruit fly behaviors. The central brain connectome is freely available online for anyone to access. When used in combination with existing methods, the map will make it easier to understand how the fly brain works, and how and why it can fail to work correctly. Many of these findings will likely apply to larger brains, including our own. In the long run, studying the fly connectome may therefore lead to a better understanding of the human brain and its disorders. Performing a similar analysis on the brain of a small mammal, by scaling up the methods here, will be a likely next step along this path.

Published
2020

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